# WinMultiPLX thermodynamic table
#
# Format: PQ/RS dH dS
# P,Q,R,S - nucleotides
# dH Enthalpy (cal/mol)
# dS Enthropy (kcal/mol*K)
#
# Source:
# Lars Kaderali
# Selecting Target Specific Probes
# for DNA Arrays
# Universitt zu Kln
# Kln, 2001
#
Energy+Enthropy
#
# Watson-Crick-Pairs
#
AA/TT -8400 -23.6
TT/AA
AC/TG -8600 -23
GT/CA
AG/TC -6100 -16.1
CT/GA
AT/TA -6500 -18.8
CA/GT -7400 -19.3
TG/AC
CC/GG -6700 -15.6
GG/CC
CG/GC -10100 -25.5
GA/CT -7700 -20.3
TC/AG
GC/CG -11100 -28.4
TA/AT -6300 -18.5
#
# A-C Mismatches
#
AA/CT 7600 20.2
TC/AA
AA/TC 2300 4.6
CT/AA
AC/CG -700 -3.8
GC/CA
AC/TA 5300 14.6
AT/CA
AG/CC 600 -0.6
CC/GA
CA/AT 3400 8
TA/AC
CA/GC 1900 3.7
CG/AC
CC/AG 5200 14.2 
GA/CC
#
# C-T Mismatches
#
AC/TT 700 0.2
TT/CA
AT/TC -1200 -6.2
CT/TA
CA/TT 1000 0.7
TT/AC
TA/CT 1200 0.7
TC/AT
CC/GT -800 -4.5
TG/CC
CC/TG 5200 13.5
GT/CC
CG/TC -1500 -6.1
CT/GC
GC/CT 2300 5.4
TC/CG
#
# G-A Mismatches
#
AA/GT 3000 7.4
TG/AA
AA/TG -600 -2.3
GT/AA
AC/GG 500 3.2
GG/CA
AG/GC -4000 -13.2
CG/GA
AG/TA -700 -2.3
AT/GA
CA/GG
GG/AC
GA/AT 700 0.7
TA/AG
GA/CG -600 -1
GC/AG
#
# G-T Mismatches
#
AG/TT 1000 0.9
TT/GA
AT/TG -2500 -8.3
GT/TA
CG/GT -4100 -11.7
TG/GC
CT/GG -2800 -8
GG/TC
GA/TT -1300 -5.3
TT/AG
GC/TG -4400 -12.3
GT/CG
GG/CT 3300 10.4
TC/GG
TA/GT -100 -1.7
TG/AT
#
# A-A Mismatches
#
AA/AT 4700 12.9
TA/AA
AA/TA 1200 1.7
AT/AA
AC/AG -2900 -9.8
GA/CA
AG/AC -900 -4.2
CA/GA
#
# C-C Mismatches
#
AC/TC 0 -4.4
CT/CA
CA/CT 6100 16.4
TC/AC
CC/CG 3600 8.9
GC/CC
CC/GC -1500 -7.2
CG/CC
#
# G-G Mismatches
#
AG/TG -3100 -9.5
GT/GA
CG/GG -4900 -15.3
GG/GC
GA/GT 1600 3.6
TG/AG
GC/GG -6000 -15.8
GG/CG
#
# T-T Mismatches
#
AT/TT -2700 -10.8
TT/TA
CT/GT -5000 -15.8
TG/TC
GT/CT -2200 -8.4
TC/TG
TA/TT 200 -1.5
TT/AT
#
# Dangling Ends
#
$A/AT -700 -0.8
TA/A$ -700 -0.8
$A/CT 4400 14.9
TC/A$
$A/GT -1600 -3.6
TG/A$
$A/TT 2900 10.4
TT/A$
$C/AG -2100 -3.9
GA/C$
$C/CG -200 -0.1
GC/C$
$C/GG -3900 -11.2
GG/C$
$C/TG -4400 -13.1
GT/C$
$T/GA -4100 -13.1
AG/T$
$G/AC -5900 -16.5
CA/G$
$G/CC -2600 -7.4
CC/G$
$G/GC -3200 -10.4
CG/G$
$G/TC -5200 -15
CT/G$
A$/TG -4200 -15
GT/$A
$T/AA -500 -1.1
AA/T$
$T/CA 4700 14.2
AC/T$
$T/TA -3800 -12.6
AT/T$
A$/TA -2900 -7.6
AT/$A
A$/TC -4100 -13
CT/$A
A$/TT -200 -0.5
TT/$A
AA/$T 200 2.3
T$/AA
AC/$G -6300 -17.1
G$/CA
AG/$C -3700 -10
C$/GA
C$/GC -4000 -11.9
CG/$C
C$/GG -3900 -10.9
GG/$C
C$/GT -4900 -13.8
TG/$C
CA/$T 600 3.3
T$/AC
CC/$G -4400 -12.6
G$/CC
G$/CG -5100 -14
GC/$G
G$/CT -4000 -10.9
TC/$G
GA/$T -1100 -1.6
T$/AG
T$/AT -6900 -20
TA/$T
#
# Double Mismatches
#
iloop 0.0 -0.97
#
# Opening and closing defaults
#
obulge_match -2660 -14.22
cbulge_match
obulge_mism 0.0 -6.45
cbulge_mism
